def requires(self): if self.pre_process_reads == "yes" and self.read_library_type == "pe": return [ bbduk(sampleName=i) for i in [ line.strip() for line in open(( os.path.join(os.getcwd(), "config", "pe_samples.lst"))) ] ] if self.pre_process_reads == "yes" and self.read_library_type == "se": return [ bbduk(sampleName=i) for i in [ line.strip() for line in open(( os.path.join(os.getcwd(), "config", "se_samples.lst"))) ] ] if self.pre_process_reads == "no" and self.read_library_type == "pe": return [ reformat(sampleName=i) for i in [ line.strip() for line in open(( os.path.join(os.getcwd(), "config", "pe_samples.lst"))) ] ] if self.pre_process_reads == "no" and self.read_library_type == "se": return [ reformat(sampleName=i) for i in [ line.strip() for line in open(( os.path.join(os.getcwd(), "config", "se_samples.lst"))) ] ]
def requires(self): if (self.pre_process_reads == "yes"): return [bbduk(sampleName=self.sampleName), makeTx2Gene()] if (self.pre_process_reads == "no"): return [reformat(sampleName=self.sampleName), makeTx2Gene()]
def requires(self): if (self.pre_process_reads == "yes"): return [ bbduk(sampleName=self.sampleName, read_library_type=self.read_library_type), makeTx2Gene(annotation_file_type=self.annotation_file_type) ] if (self.pre_process_reads == "no"): return [ reformat(sampleName=self.sampleName, read_library_type=self.read_library_type), makeTx2Gene(annotation_file_type=self.annotation_file_type) ]
def requires(self): if self.read_library_type == "pe-lr" and self.pre_process_reads=="yes": return [ [bbduk(read_library_type="pe", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [minia_pe_bbduk(os.path.join(os.getcwd(), "sample_list", "pe_samples.lst"))], [bbduk(read_library_type="lr",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]] ] if self.read_library_type == "pe-lr" and self.pre_process_reads=="no": return [ [reformat(read_library_type="pe", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [minia_pe_reformat(os.path.join(os.getcwd(), "sample_list", "pe_samples.lst"))], [reformat(read_library_type="lr",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]] ] if self.read_library_type == "pe-mp-lr" and self.pre_process_reads=="yes": return [ [bbduk(read_library_type="pe", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [bbduk(read_library_type="mp", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]], [minia_pe_mp_bbduk((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")), (os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")) )], [bbduk(read_library_type="lr",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]] ] if self.read_library_type == "pe-mp-lr" and self.pre_process_reads=="no": return [ [reformat(read_library_type="pe", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")))]], [reformat(read_library_type="mp", sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")))]], [minia_pe_mp_reformat((os.path.join(os.getcwd(), "sample_list", "pe_samples.lst")), (os.path.join(os.getcwd(), "sample_list", "mp_samples.lst")) )], [bbduk(read_library_type="lr",sampleName=i) for i in [line.strip() for line in open((os.path.join(os.getcwd(), "sample_list", "lr_samples.lst")))]] ]